Mailman 3 June 2012 - scikit-image

Re: Installing dev6.0 on windows with enthought python
by Dirk Colbry June 12, 2012

June 12, 2012

That worked great!! Thanks for all of your help and quick response. - Dirk On Tue, Jun 12, 2012 at 4:56 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > On Tue, Jun 12, 2012 at 12:25 PM, Dirk Colbry <dirkcolbry(a)gmail.com> wrote: >> I copied the file as you suggested however, it didn't seem to change >> anything, I get the same errors. Any other suggestions? Is there an >> existing email thread or google search that you suggest that may point me in >> the right direction? > > Chris just made a fix which should allow you to build successfully; > please try the latest Git version. > > Stéfan

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Re: Installing dev6.0 on windows with enthought python
by Stéfan van der Walt June 12, 2012

June 12, 2012

On Tue, Jun 12, 2012 at 12:25 PM, Dirk Colbry <dirkcolbry(a)gmail.com> wrote: > I copied the file as you suggested however, it didn't seem to change > anything, I get the same errors. Any other suggestions? Is there an > existing email thread or google search that you suggest that may point me in > the right direction? Chris just made a fix which should allow you to build successfully; please try the latest Git version. Stéfan

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Re: Installing dev6.0 on windows with enthought python
by Christoph Gohlke June 12, 2012

June 12, 2012

On 6/12/2012 12:25 PM, Dirk Colbry wrote: > > > On Monday, June 11, 2012 5:53:16 PM UTC-4, Christoph Gohlke wrote: > > On 6/11/2012 12:32 PM, Dirk Colbry wrote: > > I am struggling compiling the development version of > scikits-image in > > Windows with Enthought Python (version 27). I need the latest > version > > because our research team would like to try out the template > matching > > examples. I started by using easy_install but that just > provides for > > me the latest stable version 0.5 (not surprising). I then tried > tried > > downloading the source as described on the website. > > > > git clone http://github.com/scikits-image/scikits-image.git > <http://github.com/scikits-image/scikits-image.git> > > cd scikits-image/ > > python setup.py install > > > > The above worked fine on my Mac. However, when I tried the same > > command on a couple of different windows7 machines everything works > > until I run the python setup.py install command. It looks like > it is > > working but then it stops with the following: > > > > python setup.py install > > ... > > compile options: > '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python > > 27\lib\site-packages\numpy\core\include -IC:\Python27\include > -IC:\Python27\PC - > > c' > > gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes > -IC:\Python27\lib\site-p > > ackages\numpy\core\include > -IC:\Python27\lib\site-packages\numpy\core\include -I > > C:\Python27\include -IC:\Python27\PC -c _spath.c -o > build\temp.win-amd64-2.7\Rel > > ease\_spath.o > > Found executable C:\Python27\Scripts\gcc.exe > > gcc.exe: _spath.c: No such file or directory > > gcc.exe: no input files > > error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall > -Wstrict-prototypes -IC:\Pyt > > hon27\lib\site-packages\numpy\core\include > -IC:\Python27\lib\site-packages\numpy > > \core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c > -o build\temp.w > > in-amd64-2.7\Release\_spath.o" failed with exit status 1 > > > > > > I have the latest version of enthought python installed on all > of the > > machines. I did some searching for _spath.c and scikits-image. > There > > where a few posts but I could not find anything related to > version 6.0 > > of scikits-image. The following are a few links I found that > looked > > promising: > > > > https://github.com/stefanv/scikits.image/issues/23 > <https://github.com/stefanv/scikits.image/issues/23> > > > http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/ > <http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/> > > > > > However, none of the links I found tell me what the problem is > and how > > to fix it. The first link above, seems to indicate that the > problem > > is in Cython but I am not sure how to tell if Cython is working > (and I > > am not convinced that this is the problem). The person writing > in on > > the second link seems to have a solution but I can't figure out > what > > the solution is or how to reproduce it. Anyone have any > suggestions > > on what we can try? > > > > Thanks, > > > > - Dirk > > > > > > EPD is missing a cython.py file in the Scripts folder. Try to > manually > copy the file from > <https://github.com/cython/cython/blob/0.16/cython.py > <https://github.com/cython/cython/blob/0.16/cython.py>> to the > C:\Python27\Scripts folder. > > Christoph > > > Thanks Christoph, > > I copied the file as you suggested however, it didn't seem to change > anything, I get the same errors. Any other suggestions? Is there an > existing email thread or google search that you suggest that may point > me in the right direction? > > Thanks again, > > - Dirk I opened a pull request at <https://github.com/scikits-image/scikits-image/pull/202>. Does that work for you using a clean git clone? Christoph

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Re: Installing dev6.0 on windows with enthought python
by Christoph Gohlke June 12, 2012

June 12, 2012

On 6/12/2012 12:25 PM, Dirk Colbry wrote: > > > On Monday, June 11, 2012 5:53:16 PM UTC-4, Christoph Gohlke wrote: > > On 6/11/2012 12:32 PM, Dirk Colbry wrote: > > I am struggling compiling the development version of > scikits-image in > > Windows with Enthought Python (version 27). I need the latest > version > > because our research team would like to try out the template > matching > > examples. I started by using easy_install but that just > provides for > > me the latest stable version 0.5 (not surprising). I then tried > tried > > downloading the source as described on the website. > > > > git clone http://github.com/scikits-image/scikits-image.git > <http://github.com/scikits-image/scikits-image.git> > > cd scikits-image/ > > python setup.py install > > > > The above worked fine on my Mac. However, when I tried the same > > command on a couple of different windows7 machines everything works > > until I run the python setup.py install command. It looks like > it is > > working but then it stops with the following: > > > > python setup.py install > > ... > > compile options: > '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python > > 27\lib\site-packages\numpy\core\include -IC:\Python27\include > -IC:\Python27\PC - > > c' > > gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes > -IC:\Python27\lib\site-p > > ackages\numpy\core\include > -IC:\Python27\lib\site-packages\numpy\core\include -I > > C:\Python27\include -IC:\Python27\PC -c _spath.c -o > build\temp.win-amd64-2.7\Rel > > ease\_spath.o > > Found executable C:\Python27\Scripts\gcc.exe > > gcc.exe: _spath.c: No such file or directory > > gcc.exe: no input files > > error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall > -Wstrict-prototypes -IC:\Pyt > > hon27\lib\site-packages\numpy\core\include > -IC:\Python27\lib\site-packages\numpy > > \core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c > -o build\temp.w > > in-amd64-2.7\Release\_spath.o" failed with exit status 1 > > > > > > I have the latest version of enthought python installed on all > of the > > machines. I did some searching for _spath.c and scikits-image. > There > > where a few posts but I could not find anything related to > version 6.0 > > of scikits-image. The following are a few links I found that > looked > > promising: > > > > https://github.com/stefanv/scikits.image/issues/23 > <https://github.com/stefanv/scikits.image/issues/23> > > > http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/ > <http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/> > > > > > However, none of the links I found tell me what the problem is > and how > > to fix it. The first link above, seems to indicate that the > problem > > is in Cython but I am not sure how to tell if Cython is working > (and I > > am not convinced that this is the problem). The person writing > in on > > the second link seems to have a solution but I can't figure out > what > > the solution is or how to reproduce it. Anyone have any > suggestions > > on what we can try? > > > > Thanks, > > > > - Dirk > > > > > > EPD is missing a cython.py file in the Scripts folder. Try to > manually > copy the file from > <https://github.com/cython/cython/blob/0.16/cython.py > <https://github.com/cython/cython/blob/0.16/cython.py>> to the > C:\Python27\Scripts folder. > > Christoph > > > Thanks Christoph, > > I copied the file as you suggested however, it didn't seem to change > anything, I get the same errors. Any other suggestions? Is there an > existing email thread or google search that you suggest that may point > me in the right direction? > > Thanks again, > > - Dirk Works for me. Make sure to use a clean source directory after a failed build: either check out a new clone with git or remove the "build" directory and all *.md5 files in the skimage source directories. Christoph

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Re: Installing dev6.0 on windows with enthought python
by Christoph Gohlke June 11, 2012

June 11, 2012

On 6/11/2012 12:32 PM, Dirk Colbry wrote: > I am struggling compiling the development version of scikits-image in > Windows with Enthought Python (version 27). I need the latest version > because our research team would like to try out the template matching > examples. I started by using easy_install but that just provides for > me the latest stable version 0.5 (not surprising). I then tried tried > downloading the source as described on the website. > > git clone http://github.com/scikits-image/scikits-image.git > cd scikits-image/ > python setup.py install > > The above worked fine on my Mac. However, when I tried the same > command on a couple of different windows7 machines everything works > until I run the python setup.py install command. It looks like it is > working but then it stops with the following: > > python setup.py install > ... > compile options: '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python > 27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC - > c' > gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Python27\lib\site-p > ackages\numpy\core\include -IC:\Python27\lib\site-packages\numpy\core\include -I > C:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.win-amd64-2.7\Rel > ease\_spath.o > Found executable C:\Python27\Scripts\gcc.exe > gcc.exe: _spath.c: No such file or directory > gcc.exe: no input files > error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Pyt > hon27\lib\site-packages\numpy\core\include -IC:\Python27\lib\site-packages\numpy > \core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.w > in-amd64-2.7\Release\_spath.o" failed with exit status 1 > > > I have the latest version of enthought python installed on all of the > machines. I did some searching for _spath.c and scikits-image. There > where a few posts but I could not find anything related to version 6.0 > of scikits-image. The following are a few links I found that looked > promising: > > https://github.com/stefanv/scikits.image/issues/23 > http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/ > > However, none of the links I found tell me what the problem is and how > to fix it. The first link above, seems to indicate that the problem > is in Cython but I am not sure how to tell if Cython is working (and I > am not convinced that this is the problem). The person writing in on > the second link seems to have a solution but I can't figure out what > the solution is or how to reproduce it. Anyone have any suggestions > on what we can try? > > Thanks, > > - Dirk > > EPD is missing a cython.py file in the Scripts folder. Try to manually copy the file from <https://github.com/cython/cython/blob/0.16/cython.py> to the C:\Python27\Scripts folder. Christoph

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Installing dev6.0 on windows with enthought python
by Dirk Colbry June 11, 2012

June 11, 2012

I am struggling compiling the development version of scikits-image in Windows with Enthought Python (version 27). I need the latest version because our research team would like to try out the template matching examples. I started by using easy_install but that just provides for me the latest stable version 0.5 (not surprising). I then tried tried downloading the source as described on the website. git clone http://github.com/scikits-image/scikits-image.git cd scikits-image/ python setup.py install The above worked fine on my Mac. However, when I tried the same command on a couple of different windows7 machines everything works until I run the python setup.py install command. It looks like it is working but then it stops with the following: python setup.py install ... compile options: '-IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python 27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC - c' gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Python27\lib\site-p ackages\numpy\core\include -IC:\Python27\lib\site-packages\numpy\core\include -I C:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.win-amd64-2.7\Rel ease\_spath.o Found executable C:\Python27\Scripts\gcc.exe gcc.exe: _spath.c: No such file or directory gcc.exe: no input files error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -IC:\Pyt hon27\lib\site-packages\numpy\core\include -IC:\Python27\lib\site-packages\numpy \core\include -IC:\Python27\include -IC:\Python27\PC -c _spath.c -o build\temp.w in-amd64-2.7\Release\_spath.o" failed with exit status 1 I have the latest version of enthought python installed on all of the machines. I did some searching for _spath.c and scikits-image. There where a few posts but I could not find anything related to version 6.0 of scikits-image. The following are a few links I found that looked promising: https://github.com/stefanv/scikits.image/issues/23 http://blog.philippklaus.de/2011/08/handle-16bit-tiff-images-in-python/ However, none of the links I found tell me what the problem is and how to fix it. The first link above, seems to indicate that the problem is in Cython but I am not sure how to tell if Cython is working (and I am not convinced that this is the problem). The person writing in on the second link seems to have a solution but I can't figure out what the solution is or how to reproduce it. Anyone have any suggestions on what we can try? Thanks, - Dirk

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Re: Progress towards 0.6
by Guillaume Gay June 7, 2012

June 7, 2012

Here is what I get (with tifffile in the python path): ERROR: test suite for <module 'test_tifffile' from '/home/guillaume/Python/scikits-image/skimage/io/tests/test_tifffile.pyc'> ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 227, in run self.tearDown() File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 350, in tearDown self.teardownContext(ancestor) File "/usr/lib/python2.7/dist-packages/nose/suite.py", line 366, in teardownContext try_run(context, names) File "/usr/lib/python2.7/dist-packages/nose/util.py", line 478, in try_run return func() File "/home/guillaume/Python/scikits-image/skimage/io/tests/test_tifffile.py", line 22, in teardown sio.use_plugin(v[0], k) IndexError: list index out of range ---------------------------------------------------------------------- Ran 14 tests in 0.023s Le 07/06/2012 14:29, Tony Yu a écrit : > > > On Thu, Jun 7, 2012 at 2:30 AM, Guillaume Gay > <guillaume(a)mitotic-machine.org <mailto:guillaume@mitotic-machine.org>> > wrote: > > Hi Tony, > > The test runs fine for me... > > [guillaume]:tests $ python test_tifffile.py > SSS > > ---------------------------------------------------------------------- > Ran 3 tests in 0.001s > > OK (SKIP=3) > > > What should I do to try to reproduce? > > Guillaume > > > Hi Guillaume, > > Could you grab a copy of the tifffile source and put it on your python > path or your working directory? You can copy the body from the following: > > http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html > <http://www.lfd.uci.edu/%7Egohlke/code/tifffile.py.html> > > It's an html link, so you can't use "Save As"; you'll have to copy the > text to a text file to save it (I couldn't find a link to a *.py file). > > Thanks a lot for testing, > -Tony > > > > Le 07/06/2012 05:10, Tony Yu a écrit : > > * PR #195 to fix a test error (Can you confirm this error? I > can't see why I'd be the only one to see this error.) > https://github.com/scikits-image/scikits-image/pull/195 > > >

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Re: Progress towards 0.6
by Guillaume Gay June 7, 2012

June 7, 2012

Hi Tony, The test runs fine for me... [guillaume]:tests $ python test_tifffile.py SSS ---------------------------------------------------------------------- Ran 3 tests in 0.001s OK (SKIP=3) What should I do to try to reproduce? Guillaume Le 07/06/2012 05:10, Tony Yu a écrit : > * PR #195 to fix a test error (Can you confirm this error? I can't see > why I'd be the only one to see this error.) > https://github.com/scikits-image/scikits-image/pull/195

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Re: Progress towards 0.6
by Tony Yu June 7, 2012

June 7, 2012

On Tue, Jun 5, 2012 at 11:52 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi, everyone > > Here's a Huboard overview of scikits-image: > > http://huboard.com/scikits-image/scikits-image/board# > > Have a look at the 0.6 milestone--these are things we need to finish > up before releasing (shall we aim for Sunday?). > > Stéfan > That sounds good to me. Of the pending PRs, I'd say we should aim to merge the following: * PR #195 to fix a test error (Can you confirm this error? I can't see why I'd be the only one to see this error.) https://github.com/scikits-image/scikits-image/pull/195 * PR #194 to fix PyFITS https://github.com/scikits-image/scikits-image/pull/194 * PR #193 to make conversion between signed -> unsigned ints symmetric in dtype.convert https://github.com/scikits-image/scikits-image/pull/193 The rest are enhancements (which would be nice to have but aren't show stoppers). Of those remaining PRs, I'd say that the following are really close * PR #145, which adds `resample` https://github.com/scikits-image/scikits-image/pull/145 * PR #119, which adds SSIM https://github.com/scikits-image/scikits-image/pull/119 I'm traveling to a conference this weekend, but I should be able to help out a bit with any last minute work, if necessary. -Tony

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memory problem
by lorenzo June 6, 2012

June 6, 2012

I try to run my python program with a large matrix image. Unfortunately I receive an memory error. Here the program (that run in window PC) that donot crash with image represented by matrix 3000 x 3000. With 7000 x 7000 do not works. Even increasinf the virtual memory the problem still remain. best reg Lorenzo Bottai import skimage.graph as graph from skimage import filter from skimage.morphology import watershed, is_local_maximum from scipy import ndimage import os, numpy, sys, time,math,csv from osgeo import gdal, ogr from osgeo.gdalconst import * from math import * from gdalconst import * startTime = time.time() os.chdir(r'c:\Users\lorenzo\lidar2') # register all of the GDAL drivers gdal.AllRegister() # open the image inDs1 = gdal.Open('conv_utm2m.tif',GA_ReadOnly) print 'legge immagine di convergenza' #inDs2 = gdal.Open('htree_corretto_filt.rst',GA_ReadOnly) # get image size rows = inDs1.RasterYSize cols = inDs1.RasterXSize bands = inDs1.RasterCount transform = inDs1.GetGeoTransform() driver = gdal.GetDriverByName('GTiff') #outDs = driver.Create('origf3_flessi.tif', cols, rows, 1, GDT_Int32) outDs1 = driver.Create('conv_massimo.tif', cols, rows, 1, GDT_Int32) outDs2 = driver.Create('conv_chiome.tif', cols, rows, 1, GDT_Int32) print 'righe', rows, 'colonne', cols, 'bande', bands driver1 = inDs1.GetDriver() #driver2 = inDs2.GetDriver() convergenza = numpy.ones((rows,cols),numpy.float) massimi =numpy.zeros((rows,cols),numpy.int) chiome = numpy.zeros((rows,cols),numpy.float) inBand1 = inDs1.GetRasterBand(1) print 'leggo convergenza' convergenza = inBand1.ReadAsArray(0,0,cols,rows).astype(numpy.float) print ' cerco il massimo locale sulla convergenza' massimi = is_local_maximum(convergenza) print ' numero in modo progressimo i massimi' markers = ndimage.label(massimi)[0] print ' allago le pozze ........' chiome = watershed(-convergenza, markers) outBand1 = outDs1.GetRasterBand(1) outBand2 = outDs2.GetRasterBand(1) outBand1.WriteArray(massimi, 0, 0) outBand1.FlushCache() stats1 = outBand1.GetStatistics(0, 1) outBand2.WriteArray(chiome, 0, 0) outBand2.FlushCache() stats2 = outBand2.GetStatistics(0, 1) outDs1.SetGeoTransform(transform) outDs2.SetGeoTransform(transform) outDs1 = None outDs2 = None inDs1 = None print 'script took', time.time() - startTime, 'seconds to run'

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